[BioC] limma question

Gordon Smyth smyth at wehi.edu.au
Sat Sep 13 12:02:00 MEST 2003

At 12:23 AM 13/09/2003, Straubhaar, Juerg wrote:
>I'm reading smd file into limma and would like to give weight of zero to
>spots with FLAG != 0 (-50 in my file). I type the following:
>*       RG<-read.maimages("/home/jstraubh/mello/data/cex211.xls",
>source="smd", wt.fun=wtflags(0), fill=T)

1. Have you checked that this command works without use of the 'wt.fun' 
argument? The fact that your data file has an 'xls' extension suggests that 
it is an excel spreadsheet. If this is the case, you need to use excel to 
save your file as tab-delimited text. Like most read commands in R, 
read.maimages() is designed to read text files, not proprietry binary formats.

2. The function wtflags() is only for Genepix data, see ?wt.flags. If you 
have a column of your data file called "FLAG", then you need

    wt.fun = function(x) x$FLAG >= 0

For example,

   RG <- read.maimages(filenames, source="smd", wt.fun= function(x) 
x$FLAG >= 0)


>After entering this generates an error:
>Error in "[<-"(*tmp*, , i, value = numeric(0)) :
>        nothing to replace with
>Thank you for your help.
>Juerg Straubhaar,
>University of Massachusetts Medical School

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